Job ID = 6453448 SRX = SRX1150356 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:27:26 prefetch.2.10.7: 1) Downloading 'SRR2164523'... 2020-06-21T08:27:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:34 prefetch.2.10.7: 'SRR2164523' is valid 2020-06-21T08:28:34 prefetch.2.10.7: 1) 'SRR2164523' was downloaded successfully 2020-06-21T08:29:26 prefetch.2.10.7: 'SRR2164523' has 10 unresolved dependencies 2020-06-21T08:29:26 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:29:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:39 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:29:39 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:29:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:55 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:29:55 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:29:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:53 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:53 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:31:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:15 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:15 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:32:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:32 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:32 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:32:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:48 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:48 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:32:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:08 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:08 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:33:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:20 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:20 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:34 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:34 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:33:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:48 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 5390311 spots for SRR2164523/SRR2164523.sra Written 5390311 spots for SRR2164523/SRR2164523.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:40 5390311 reads; of these: 5390311 (100.00%) were unpaired; of these: 98588 (1.83%) aligned 0 times 3310717 (61.42%) aligned exactly 1 time 1981006 (36.75%) aligned >1 times 98.17% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 435878 / 5291723 = 0.0824 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:37:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:36: 1000000 INFO @ Sun, 21 Jun 2020 17:37:41: 2000000 INFO @ Sun, 21 Jun 2020 17:37:46: 3000000 INFO @ Sun, 21 Jun 2020 17:37:52: 4000000 INFO @ Sun, 21 Jun 2020 17:37:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:37:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:37:57: #1 total tags in treatment: 4855845 INFO @ Sun, 21 Jun 2020 17:37:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:37:57: #1 tags after filtering in treatment: 4855708 INFO @ Sun, 21 Jun 2020 17:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:58: #2 number of paired peaks: 1418 INFO @ Sun, 21 Jun 2020 17:37:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:58: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:37:58: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 17:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05_model.r WARNING @ Sun, 21 Jun 2020 17:37:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:58: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 17:37:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:37:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:58: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:38:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:06: 1000000 INFO @ Sun, 21 Jun 2020 17:38:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:13: 2000000 INFO @ Sun, 21 Jun 2020 17:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:13: Done! pass1 - making usageList (590 chroms): 1 millis pass2 - checking and writing primary data (2366 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:20: 3000000 INFO @ Sun, 21 Jun 2020 17:38:26: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:38:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:32: #1 total tags in treatment: 4855845 INFO @ Sun, 21 Jun 2020 17:38:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:38:33: #1 tags after filtering in treatment: 4855708 INFO @ Sun, 21 Jun 2020 17:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:33: #2 number of paired peaks: 1418 INFO @ Sun, 21 Jun 2020 17:38:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:33: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:38:33: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 17:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10_model.r WARNING @ Sun, 21 Jun 2020 17:38:33: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:38:33: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 17:38:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:38:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:37: 1000000 INFO @ Sun, 21 Jun 2020 17:38:43: 2000000 INFO @ Sun, 21 Jun 2020 17:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:49: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:50: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:58: 4000000 INFO @ Sun, 21 Jun 2020 17:39:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:03: #1 total tags in treatment: 4855845 INFO @ Sun, 21 Jun 2020 17:39:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:03: #1 tags after filtering in treatment: 4855708 INFO @ Sun, 21 Jun 2020 17:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:04: #2 number of paired peaks: 1418 INFO @ Sun, 21 Jun 2020 17:39:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:04: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:39:04: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 17:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20_model.r WARNING @ Sun, 21 Jun 2020 17:39:04: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:39:04: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 17:39:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:39:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1150356/SRX1150356.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:20: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 7 millis CompletedMACS2peakCalling